I believe the reason the EPA reinterpreted the existing law to apply to aftermarket tuning and certain delete devices is VW/Dieselgate.
The EPA realized the laws can easily be circumvented and took a deep look into them. Obviously OEM was primary but once you get down the rabbit hole there is no going back. Exhaust, software, ect. They aren't looking into quantity, they are simply looking into the fact that the 'law' was broken.
If the goal was to reduce total emissions, absolutely, they SHOULD be looking at fleet trucks, marine, military, and the oodles of other sources that burn magnitudes more fuel than hobbyist motorsports but they don't care, it's either out of their jurisdiction or their focus. Their goal is to enforce law on the books and what their jurisdiction is.
The big drive behind fleet diesel delete is the immense cost of replacement. When it adds no (and actually subtracts) efficiency, and increases cost while providing zero financial benefit to the owner and increase downtime, of course people are going to delete it even if it is illegal.
If the govt provided or mandated lifetime warranty on highway emission components I think a lot of people would not do deletes, but when it costs $5-$8k in parts plus labor to keep the system working, and it costs 1/3 or less do delete, it's not surprising. Especially when powertrain warranties are in the 50-100k range and emission component warranties are 1/4 to 1/2 as long.
Necessity is the mother of invention.